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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T10","span":{"begin":993,"end":1006},"obj":"Body_part"}],"attributes":[{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_0034922"}],"text":"Fig. 3 CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, J) Each dot represents an individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 patient (red). Significance determined by unpaired Wilcoxon test with BH correction: *p \u003c 0.05, **p \u003c 0.01, ***p \u003c 0.001, and ****p \u003c 0.0001."}

LitCovid-PubTator

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T154","span":{"begin":45,"end":53},"obj":"Disease"},{"id":"T155","span":{"begin":325,"end":327},"obj":"Disease"},{"id":"T156","span":{"begin":464,"end":472},"obj":"Disease"},{"id":"T157","span":{"begin":568,"end":570},"obj":"Disease"},{"id":"T158","span":{"begin":706,"end":714},"obj":"Disease"},{"id":"T159","span":{"begin":836,"end":838},"obj":"Disease"},{"id":"T160","span":{"begin":840,"end":842},"obj":"Disease"},{"id":"T161","span":{"begin":848,"end":856},"obj":"Disease"},{"id":"T162","span":{"begin":1281,"end":1283},"obj":"Disease"},{"id":"T163","span":{"begin":1310,"end":1312},"obj":"Disease"},{"id":"T164","span":{"begin":1324,"end":1332},"obj":"Disease"},{"id":"T165","span":{"begin":1403,"end":1405},"obj":"Disease"}],"attributes":[{"id":"A154","pred":"mondo_id","subj":"T154","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A155","pred":"mondo_id","subj":"T155","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A156","pred":"mondo_id","subj":"T156","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A157","pred":"mondo_id","subj":"T157","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A158","pred":"mondo_id","subj":"T158","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A159","pred":"mondo_id","subj":"T159","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A160","pred":"mondo_id","subj":"T160","obj":"http://purl.obolibrary.org/obo/MONDO_0009973"},{"id":"A161","pred":"mondo_id","subj":"T161","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A162","pred":"mondo_id","subj":"T162","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A163","pred":"mondo_id","subj":"T163","obj":"http://purl.obolibrary.org/obo/MONDO_0009973"},{"id":"A164","pred":"mondo_id","subj":"T164","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A165","pred":"mondo_id","subj":"T165","obj":"http://purl.obolibrary.org/obo/MONDO_0010873"}],"text":"Fig. 3 CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, J) Each dot represents an individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 patient (red). Significance determined by unpaired Wilcoxon test with BH correction: *p \u003c 0.05, **p \u003c 0.01, ***p \u003c 0.001, and ****p \u003c 0.0001."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T116","span":{"begin":325,"end":327},"obj":"Chemical"},{"id":"T117","span":{"begin":506,"end":508},"obj":"Chemical"},{"id":"T118","span":{"begin":568,"end":570},"obj":"Chemical"},{"id":"T119","span":{"begin":618,"end":620},"obj":"Chemical"},{"id":"T120","span":{"begin":836,"end":838},"obj":"Chemical"},{"id":"T121","span":{"begin":840,"end":842},"obj":"Chemical"},{"id":"T122","span":{"begin":933,"end":940},"obj":"Chemical"},{"id":"T123","span":{"begin":1274,"end":1279},"obj":"Chemical"},{"id":"T124","span":{"begin":1281,"end":1283},"obj":"Chemical"},{"id":"T125","span":{"begin":1303,"end":1308},"obj":"Chemical"},{"id":"T126","span":{"begin":1310,"end":1312},"obj":"Chemical"}],"attributes":[{"id":"A116","pred":"chebi_id","subj":"T116","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A117","pred":"chebi_id","subj":"T117","obj":"http://purl.obolibrary.org/obo/CHEBI_73445"},{"id":"A118","pred":"chebi_id","subj":"T118","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A119","pred":"chebi_id","subj":"T119","obj":"http://purl.obolibrary.org/obo/CHEBI_73445"},{"id":"A120","pred":"chebi_id","subj":"T120","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A121","pred":"chebi_id","subj":"T121","obj":"http://purl.obolibrary.org/obo/CHEBI_73812"},{"id":"A122","pred":"chebi_id","subj":"T122","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A123","pred":"chebi_id","subj":"T123","obj":"http://purl.obolibrary.org/obo/CHEBI_17891"},{"id":"A124","pred":"chebi_id","subj":"T124","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A125","pred":"chebi_id","subj":"T125","obj":"http://purl.obolibrary.org/obo/CHEBI_17891"},{"id":"A126","pred":"chebi_id","subj":"T126","obj":"http://purl.obolibrary.org/obo/CHEBI_73812"}],"text":"Fig. 3 CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, J) Each dot represents an individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 patient (red). Significance determined by unpaired Wilcoxon test with BH correction: *p \u003c 0.05, **p \u003c 0.01, ***p \u003c 0.001, and ****p \u003c 0.0001."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T54","span":{"begin":12,"end":29},"obj":"http://purl.obolibrary.org/obo/GO_0042110"},{"id":"T55","span":{"begin":14,"end":29},"obj":"http://purl.obolibrary.org/obo/GO_0001775"}],"text":"Fig. 3 CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, J) Each dot represents an individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 patient (red). Significance determined by unpaired Wilcoxon test with BH correction: *p \u003c 0.05, **p \u003c 0.01, ***p \u003c 0.001, and ****p \u003c 0.0001."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T134","span":{"begin":0,"end":107},"obj":"Sentence"},{"id":"T135","span":{"begin":108,"end":329},"obj":"Sentence"},{"id":"T136","span":{"begin":330,"end":572},"obj":"Sentence"},{"id":"T137","span":{"begin":573,"end":1197},"obj":"Sentence"},{"id":"T138","span":{"begin":1198,"end":1347},"obj":"Sentence"},{"id":"T139","span":{"begin":1348,"end":1474},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Fig. 3 CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, J) Each dot represents an individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 patient (red). Significance determined by unpaired Wilcoxon test with BH correction: *p \u003c 0.05, **p \u003c 0.01, ***p \u003c 0.001, and ****p \u003c 0.0001."}

PMC:7402624 / 21566-23040 JSONTXT

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PMC:7402624 / 21566-23040 JSON TXT